Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID

Abstract

The epidermis of Caenorhabditis elegans is an essential tissue for survival as it contributes to the formation of the cuticle barrier, as well as facilitates developmental progression and animal growth. Most of the epidermis consists of the hyp7 hypodermal syncytium, the nuclei of which are largely generated by the seam cells that exhibit stem cell-like behaviour during development. How the seam cell progenitors differ transcriptionally from the differentiated hypodermis is poorly understood. Here, we introduce Targeted DamID (TaDa) in C. elegans as a method for identifying genes expressed within a tissue of interest without cell isolation. We show that TaDa signal enrichment profiles can be used to identify genes transcribed in the epidermis and use this method to resolve differences in gene expression between the seam cells and the hypodermis. We finally predict and functionally validate new transcription and chromatin factors acting in seam cell development. These findings provide insights into cell-type-specific gene expression profiles likely associated with epidermal cell fate patterning.

A transient apical extracellular matrix relays cytoskeletal patterns to shape permanent acellular ridges on the surface of adult C. elegans

“…elegans genes encode actin monomers. During the L4 stage, epidermal cells and syncytia express act-2 most highly, with some evidence for expression of act-1 , -3 and -4 at other stages [ 33 , 34 ]. To simultaneously knock down act-1 , -2 , -3 and -4 , we selected an act-2 -derived dsRNA trigger complementary to all four transcripts ( Materials and Methods ).…”

Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in C. elegans

“…Various methods are available for analysis of gene expression profiles in specific cell types in C. elegans, including physical isolation of cells or nuclei of interest [65–67], affinity purification of RNAs from specific cells [68], trans-splicing-based RNA tagging [69], and mapping of RNA polymerase occupancy [14,70]. While each of these methods present advantages and limitations, none of them allows the specific identification of nascent transcripts at a particular time point during development.…”

“…To illustrate the reproducibility of the method, T>C fractions of 4 genes reported to be expressed in the hypodermis are shown (pars-1, mig-15, dpy-3 and nhr-97; FDR<0.03; Figure 7D). Finally, to evaluate the specificity of SLAM-ITseq, we compared the list of 197 nascent transcripts to three datasets of genes reported to be expressed in the hypodermis [70,67,68] (Figure 7E). Our list overlapped significantly with all three datasets (168/197 = 85%; p<1e-10 Fisher’s exact test), which represents the second highest overlap.…”

“…We could not compare our list from SLAM-ITseq to the RAPID method because different tissues were analyzed. Instead, we compared our list with hypodermal data from another recent DamID-based (TaDa) study [70] and found a significant overlap (p=1.6e-11). We also found significant overlaps when comparing our data with hypodermal lists from two other methods, PATseq [68] and FACS [67] (p<2.2e-16).…”

Transcription factors regulating the fate and developmental potential of a multipotent progenitor in C. elegans

“…It is most similar to two mammalian genes, E2F7 and E2F8, and was identified for its ability to inhibit cell death in ventral cord neurons by promoting expression of the pro-apoptotic gene egl-1 (Winn et al, 2011). It is also expressed in seam cell lineages and is required for development of the correct number of seam cells in the adult (Katsanos et al, 2021). We show here that loss of efl-3 function in the somatic gonad results in one or two additional DTCs.…”